if you updated the IP address in the previous step: restart rabbitmq server

sudo pkill -U rabbitmq
sudo /etc/init.d/rabbitmq-server start

start cloudman script

sudo sh /mnt/cm/run.sh --daemon

go to http://galaxy.nbic.nl/cloud and login with admin/{default password} to initiate the launch of cloud Galaxy. When it asks you for the 'initial storage' just ignore this and click on the 'cloudman' button at the bottom of the pop-up.

Update database

Configure the new galaxy: we keep the all the files (datasets) associated with histories stored in the Postgres database in a separate database folder outside the galaxy root folder.

cd /mnt/galaxyTools/galaxy-central
rmdir database
# Note: make sure this is the EMPTY database folder of the new install and not
# a symlink pointing to our data in /opt/galaxy/data/database/
ln -s /mnt/galaxyData/database database

Copy NBIC tools and data

Customize the new Galaxy: We keep copies of modified (config) files in the conerice repository. You should diff our customized versions in the conerice repo with the new versions in Galaxy. When necessary merge updates from the Galaxy developers with our local customizations and commit a new version to the conerice repo. If there are no changes you can simply copy the files below:

Always use a strong password on user accounts (8 or more characters and use letters, numbers and specials). Set the initial password with

sudo passwd user

When you create an account and have to e-mail the password to the user enforce a password change on first use with the following command:

sudo chage -d 0 user

When you are giving temporary access to someone set an expiration date for the account with the following command:

sudo chage -E YYYY-MM-DD user

make sure the user is member of the right groups. Users who need to have access to galaxy need to be in the devs group, but only give group membership if it is really necessary. Anyone who is member of the devs group can potentially break stuff...

To change the group memberships later on you can use the following command: